Dataset Information

The small protein CdrS is involved in cell division regulation

ABSTRACT: Recently the function and cellular importance of small proteins became more and more visible. Whereas many examples of small protein functions have been described in eukarya and bacteria, less is known about small protein functions in archaea. A previous determination of the proteome in the halophilic archaeon Haloferax volcanii by mass spectrometry confirmed the expression of several annotated genes for small proteins. One such protein is encoded by HVO_0582. To identify the biological function of the encoded small protein we attempted to generate a deletion strain. Since we were not successful in generating the deletion we repressed HVO_0582 using CRISPRi. The repression strain showed a severe growth defect as well as strong changes in morphology. ChIPSeq experiments revealed several binding sites for this putative transcription factor. Transcriptome and proteome analyses show a clear effect on RNA and protein expression in the CRISPRi strain. Based on our findings we conclude that the small protein CdrS is involved in regulation of cell division / cell morphology.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Haloferax Volcanii (halobacterium Volcanii)

SUBMITTER: Sandra Maass

LAB HEAD: Dörte Becher

PROVIDER: PXD017903 | Pride | 2021-08-09

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	181108_QE1_PM1_ThS_SPP_2018_026_D_2_DIA_SN_TR_01.raw	Raw
	181108_QE1_PM1_ThS_SPP_2018_026_D_2_DIA_SN_TR_02.raw	Raw
	181108_QE1_PM1_ThS_SPP_2018_026_D_2_DIA_SN_TR_03_181112152848.raw	Raw
	181108_QE1_PM1_ThS_SPP_2018_026_WT_DIA_SN_TR_01.raw	Raw
	181108_QE1_PM1_ThS_SPP_2018_026_WT_DIA_SN_TR_02.raw	Raw

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Publications

CdrS Is a Global Transcriptional Regulator Influencing Cell Division in Haloferax volcanii.

Liao Yan Y Vogel Verena V Hauber Sabine S Bartel Jürgen J Alkhnbashi Omer S OS Maaß Sandra S Schwarz Thandi S TS Backofen Rolf R Becher Dörte D Duggin Iain G IG Marchfelder Anita A

mBio 20210713 4

Transcriptional regulators that integrate cellular and environmental signals to control cell division are well known in bacteria and eukaryotes, but their existence is poorly understood in archaea. We identified a conserved gene (cdrS) that encodes a small protein and is highly transcribed in the model archaeon Haloferax volcanii. The cdrS gene could not be deleted, but CRISPR interference (CRISPRi)-mediated repression of the cdrS gene caused slow growth and cell division de ...[more]

PMID: 34253062

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Project description:Strains of Pseudomonas putida have emerged as promising biocatalysts for the conversion of sugars and aromatics obtained from lignocellulosic biomass. Understanding the role of carbon catabolite repression (CCR) in these strains is critical to optimizing the conversion of biomass to fuels and chemicals. The functioning of CCR in a P. putida strain, P. putida M2, capable of growing on both hexose and pentose sugars as well as aromatics, was investigated by cultivation experiments, proteomics, and CRISPRi-based gene repression. Strain M2 was able to co-utilize sugars and aromatics simultaneously; however, during co-cultivation with glucose and phenylpropanoid aromatics (p-coumarate and ferulate), intermediates (4-hydroxybenzoate and vanillate) accumulated, and substrate consumption was incomplete. In contrast, xylose-aromatic consumption resulted in transient intermediate accumulation and complete aromatic consumption, while xylose was incompletely consumed. Proteomics analysis of these co- cultivations revealed that glucose exerted stronger repression compared to xylose on the proteins involved in aromatic catabolism. Key glucose (Eda) and xylose (XylX) catabolic proteins were also identified at lower abundance during co-cultivation with aromatics implying simultaneous catabolite repression by sugars and aromatics. Downregulation of crc mediated by CRISPRi led to faster growth and uptake of both glucose and p-coumarate in the CRISPRi strains compared to the control while no difference was observed on xylose + p-coumarate. The increased abundance of the Eda protein and amino acids biosynthesis proteins in the CRISPRi strain further supported these observations. Lastly, small RNAs (sRNAs) sequencing results showed that the levels of CrcY and CrcZ homologs in M2, previously identified as sRNAs involved in CCR in P. putida strains, were lower under strong CCR (glucose + p-coumarate) condition compared to when repression was absent (p-coumarate or glucose only).